Cura can give you only an estimation of the print time and it normally differ from the real one. Different materials melt at different temperatures and time periods, and this also has an impact on Cura calculations. The sum of these two factors must be one of those responsible for the difference.
I believe that Cura uses higher travel move speeds and calculates from these speeds.
But the actual speed of your printer is determined by the firmware you are using.
Different materials have different melting temperatures, but also different flow rates, which results in different feedrates of the 3D printer's extruders, in order to obtain substrate layers with the required thickness and density. You can check that easily, if for the same 3D model you get change the material from PLA to ABS for example. Before do this you can check the Infill and Wall feedrate speeds in the "Speed" section in Custom Print settings.
For PLA they are 50 and 40 mm/sec respectively (these values are relevant if Ultimaker 2+ 3D printer is selected), but if only change the material to ABS, they also will be changed to 45 and 30 mm/sec respectively. Therefore, if you use PLA for print your model the time will be shorter than if you use ABS for the same thing.